Scaling Down SAGE: from miniSAGE to microSAGE

Datson, N. A.
October 2008
Current Pharmaceutical Biotechnology;Oct2008, Vol. 9 Issue 5, p351
Academic Journal
Since Serial Analysis of Gene Expression (SAGE) was introduced more than a decade ago, it has been widely applied to characterise gene expression profiles in various tissues, cell types and cell lines of diverse origin including human, mouse, rat, yeast, plant and parasites. Throughout the past years many modifications to the original SAGE protocol have been developed, which address several aspects of SAGE, including an increase in sequencing efficiency (deep-SAGE), improved tag-to-transcript mapping of SAGE tags (LongSAGE) and a reduction of the amount of required input RNA (microSAGE). Furthermore, the applications of SAGE have expanded from exclusively transcriptome analysis to now also include genome analysis, identifying genome signature tags that pinpoint transcription factor binding sites throughout the genome (Serial Analysis of Chromatin Occupancy or SACO). The review gives an overview of the main modifications to the SAGE technology that have been developed in the last decade, with a particular focus on the large reduction in the amount of required input RNA that has been achieved in the many SAGE modifications for downscaling or miniaturisation of SAGE (including microSAGE, PCR-SAGE and small amplified RNA-SAGE). The available methods for downscaling or miniaturisation of SAGE and their specific features will be discussed, illustrated by some examples of their application. This reduction in required quantity of input RNA has greatly expanded the possible applications of SAGE, allowing characterisation of global gene expression in material obtained from needle biopsies, small anatomical structures and specific cell types isolated by fluorescence activated cell sorting or laser microdissection.


Related Articles

  • Comprehensive Analysis of Glucan Elicitor-Regulated Gene Expression in Tobacco BY-2 Cells Reveals a Novel MYB Transcription Factor Involved in the Regulation of Phenylpropanoid Metabolism. Tomonori Shinya; Ivan Gális; Tomoko Narisawa; Mami Sasaki; Hiroo Fukuda; Hideaki Matsuoka; Mikako Saito; Ken Matsuoka // Plant & Cell Physiology;Oct2007, Vol. 48 Issue 10, p1404 

    We previously demonstrated that a β-1,3-, 1,6-oligoglucan (AaGlucan) from the fungus Alternaria alternata 102 shows strong elicitor activity in tobacco BY-2 cells. We have used cDNA microarray analysis to monitor global changes in gene expression in tobacco cells treated with this A....

  • Expression of the Thimet Oligopeptidase Gene is Regulated by Positively and Negatively Acting Elements. McCool, Suzan; Pierotti, Adrian R. // DNA & Cell Biology;Dec2000, Vol. 19 Issue 12, p729 

    Thimet oligopeptidase (TOP) is a thiol-dependent metallopeptidase, which can cleave and thereby modulate the activity of many neuropeptides. The enzyme is active in many endocrine tissues, including testis, brain, and pituitary. In rat, the richest source of TOP is the testes, with a specific...

  • c-Myc: Linking Transformation and Genomic Instability. Prochownik, Edward V. // Current Molecular Medicine;Sep2008, Vol. 8 Issue 6, p446 

    CMYC has long been known to be among the most frequently de-regulated oncogenes in human cancer. Only recently, however has a clear understanding begun to emerge of how it promotes transformation. Through its role as a transcription factor, c-Myc alters the expression of hundreds of target...

  • Regulation of the transcription factor GATA-1 at the gene and protein level. Tang, X. -B.; Liu, D. -P.; Liang, C. -C. // Cellular & Molecular Life Sciences;Dec2001, Vol. 58 Issue 14, p2008 

    GATA-1, an important hematopoietic transcription factor, plays a critical role in differentiation and maturation of erythroid and megakaryocytic cell lines. GATA-1 appears to serve as a factor for virtually all characterized erythroid and megakaryocytic-expressed genes. Thus, defining the...

  • G-protein-coupled receptor participates in 20- hydroxyecdysone signaling on the plasma membrane. Mei-Juan Cai; Du-Juan Dong; Yu Wang; Peng-Cheng Liu; Wen Liu; Jin-Xing Wang; Xiao-Fan Zhao // Cell Communication & Signaling;2014, Vol. 12 Issue 1, p1 

    Background Animal steroid hormones are conventionally known to initiate signaling via a genomic pathway by binding to the nuclear receptors. The mechanism by which 20E initiates signaling via a nongenomic pathway is unclear. Results We illustrate that 20E triggered the nongenomic pathway through...

  • A Functional Enhancer of Keratin14 Is a Direct Transcriptional Target of ΔNp63. Romano, Rose-Anne; Birkaya, Barbara; Sinha, Satrajit // Journal of Investigative Dermatology;May2007, Vol. 127 Issue 5, p1175 

    Keratin14 (K14) is a prototypic marker of dividing basal keratinocytes where its gene is transcribed at high levels. Transcriptional regulation of K14 is governed by an evolutionarily conserved functional enhancer marked by DNase 1 hypersensitive sites present upstream of the gene. This enhancer...

  • Characterization of functional elements in the neurofibromatosis (NF1) proximal promoter region. Min-Xu Zou; Butcher, Darci T.; Sadikovic, Bekim; Groves, Timothy C.; Siu-Pok Yee; Rodenhiser, David I. // Oncogene;1/15/2004, Vol. 23 Issue 2, p330 

    An essential requirement to understand how genes contribute to genetic disease is the thorough knowledge of the transcriptional regulation of gene expression. Here, we have characterized transcription factor binding sites within the type 1 neurofibromatosis (NF1) proximal regulatory region, and...

  • Overexpression of Kruppel-like factor 4 in the human colon cancer cell line RKO leads to reduced tumorigenecity. Dang, Duyen T; Chen, Xinming; Feng, Jing; Torbenson, Michael; Dang, Long H; Yang, Vincent W // Oncogene;5/29/2003, Vol. 22 Issue 22, p3424 

    Kruppel-like factor 4 (KLF4) is a zinc-finger-containing transcription factor, the expression of which is enriched in the postmitotic cells of the intestinal epithelium. KLF4 is a target gene of the tumor suppressor adenomatous polyposis coli (APC). We sought to determine the role of KLF4 in...

  • Gene regulation: Fine-tuned amplification in cells. Dang, Chi V. // Nature;7/24/2014, Vol. 511 Issue 7510, p417 

    The article focuses on studies on regulation of gene expression by transcription factor Myc by researcher A. Sabò and S. Walz. It mentions that Walz used human cell lines for experimentally manipulating Myc expression and Sabò used mouse cell line for Myc expression. It also mentions that...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics